PhD Position - C++ Software Engineering of a 3D Cell-Based Tissue Simulation Framework 100%, Basel, fixed-term

PhD Position - C++ Software Engineering of a 3D Cell-Based Tissue Simulation Framework

100%, Basel, fixed-term

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The Computational Biology (CoBi) group, led by Prof. Dagmar Iber, develops data-driven, mechanistic models of
biological systems using advanced imaging and computational tools. Our group combines biology, engineering, and
computational science to understand how cells organize into complex tissues. Located in Basel, the Department of
Biosystems Science and Engineering (D-BSSE) provides a vibrant research environment at the interface of biology,
engineering, and medicine, and is surrounded by leading pharmaceutical and biotech companies. ETH Zurich is a
world-leading university dedicated to advancing science and technology.

Project background

We are seeking a highly motivated PhD student to contribute to the further development of SimuCell3D , a
high-performance C++ framework for simulating 3D tissues of thousands deformable cells—including extracellular matrix
and cavities—within a single day [Runser et al., 2024, Nat Comput Sci 4, 299–309; Tweetorial]. This platform allows
investigation of tissue mechanics, cell polarization, and morphogenetic processes at unprecedented scale.

Job description

Your role will include:

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Extending SimuCell3D with advanced numerical solvers for reaction-diffusion systems

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Enhancing the biophysical capabilities of the C++ framework

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Applying the framework to morphogenetic questions using real imaging data

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Running large-scale simulations on ETH’s HPC infrastructure

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Calibrating models, performing parameter screens, and validating predictions against experimental data

Profile

We are looking for candidates with:

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Strong computational skills in C++ and software engineering

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Strong background in computational science, applied mathematics, or computational biology

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Ideally, familiarity with numerical methods for PDEs (e.g., finite difference, finite element)

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HPC experience is a plus but not required

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Interest in biophysics, developmental biology, or cell signaling (no prior experience required)

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Independent, proactive, and structured work style

Master’s students interested in starting with a thesis project on this topic are also encouraged to apply.

Workplace

Workplace

We offer

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Fully funded PhD with internationally competitive salary and comprehensive benefits, in accordance with ETH Zurich
guidelines

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Access to ETH’s HPC clusters and state-of-the-art research infrastructure

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Supportive, interdisciplinary research environment

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Flexible home office arrangements

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Numerous benefits, such as public transport season tickets and car sharing, a wide range of sports offered by the
ASVZ, childcare and attractive pension benefits

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We value diversity and sustainability

In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value
diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students
are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open
environment that allows everyone to grow and flourish. Sustainability is a core value for us – we are consistently
working towards a climate-neutral future.

Curious? So are we.

We look forward to receiving your online application with the following documents:

- Letter of Motivation
- CV
- Diplomas & Transcripts
- Contact details of 2 referees

Please note that we exclusively accept applications submitted through our online application portal. Applications via
email or postal services will not be considered.

Further information about the group can be found on our website. Questions regarding the position should be directed
to Prof Iber by e-mail: iberd@ethz.ch (no applications).

About ETH Zürich

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our
excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000
people from more than 120 countries find our university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we
work together to develop solutions for the global challenges of today and tomorrow.

About ETH Zürich

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our
excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000
people from more than 120 countries find our university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we
work together to develop solutions for the global challenges of today and tomorrow.